Egypt's highest prosecutor on Thursday called for the release of political prisoners who were held during the rule of the now embattled Muslim Brotherhood but the official spokesperson for the Islamist movement warned that Egypt was on the brink of becoming a "police state" after the arrest of its leader hours earlier. Mana Rabiee reports.

EGYPT'S interim president Adli Mansour has been sworn in after the overthrow of Mohamed Morsi.

The Egyptian judge, who was chosen as interim president by armed forces, has taken his oath as head of the constitutional court.

He will lead the nation until the next presidential elections.

Dressed in a dark blue suit and blue tie, Mr Mansour used his first remarks as interim leader to praise the massive street demonstrations that led to Mr Morsi's ouster. He also hailed the youth behind the protests that began on June 30.

"The most glorious thing about June 30 is that it brought together everyone without discrimination or division," he said. "I offer my greetings to the revolutionary people of Egypt."

Egypt's chief justice Adli Mansour pauses during his swearing-in ceremony as Egypt's interim president in the Supreme Constitutional Court in Cairo.

"I look forward to parliamentary and presidential elections held with the genuine and authentic will of the people," Mr Mansour said. "The youth had the initiative and the noblest thing about this glorious event is that it was an expression of the nation's conscience and an embodiment of its hopes and ambitions. It was never a movement seeking to realise special demands or personal interests."

The revolution, he said, must continue, so "we stop producing tyrants."

Mr Mansour replaced Mr Morsi, who was Egypt's first democratically elected president but was overthrown by the military on Wednesday after a tumultuous year in office. Mr Morsi is under house arrest at an undisclosed location.

And in the highest profile arrest since Mr Morsi's ouster, security officials said that Mohammed Badie, supreme leader of the Brotherhood, was arrested late on Wednesday in the Mediterranean coastal city of Marsa Matrouh, where he has been staying in a villa owned by a businessman with Brotherhood links.

Egyptian national flags are waved as hundreds of thousands demonstrate against President Mohammed Morsi and the Muslim brotherhood outside the Egyptian presidential palace on July 3, 2013 in Cairo, Egypt. AFP PHOTO / MAHMOUD KHALED

He was flown to Cairo on a military helicopter, according to the officials, who spoke on condition of anonymity because they were not authorized to speak to the media. He, and his powerful deputy, Khairat el-Shater, are wanted for questioning on their role in the killing this week of eight protesters in clashes outside the Brotherhood's Cairo headquarters.

Egyptians woke up to a new day after armed forces ousted Mr Morsi, and up to 14 died in the clashes.

Mohamed Morsi remains detained in a military facility with top aides after the army announced his ouster, a senior member of the Muslim Brotherhood said.

"Morsi and the entire presidential team are under house arrest in the Presidential Republican Guards Club," Gehad El-Haddad, the son of a top Morsi aide, told AFP.

Egyptian women shout slogans against President Mohammed Morsi as Egyptian national flags are waved as hundreds of thousands demonstrate against him in Cairo, Egypt. AFP PHOTO / MAHMOUD KHALED

"Morsi has been separated from his aides and was taken to the defence ministry,'' he said.

Haddad's father, Essam El-Haddad, widely seen as Mr Morsi's right-hand man, was among those held, he added.

The Egyptian military has confirmed it is holding Mr Morsi. It was not immediately clear whether the ousted president would later be allowed to leave.

Up to 14 people have been killed in clashes in several Egyptian cities between opponents and supporters of the deposed president, Al Jazeera television has reported, citing state media and local officials.

WARNING Graphic Content: This video shows a man being shot in the city of Alexandria, though it is not clear from the video where the shot came from.
It has been widely shared on social networks in Egypt. Credit: youtube/storyful/elsayed ezz

Eight people, including members of the security forces, were reported to have died in clashes in the northern city of Marsa Matrouh. Casualties were also reported in the port city of Alexandria, Minya in southern Egypt and Fayoum, south of Cairo.

His top aides have switched off their phones. Other presidential aides who were separated from Mr Morsi earlier in the day say they have lost communication with their leader.

Mr Morsi had earlier been at his office in the Republican Guard's headquarters, before he was moved.

An Egyptian family celebrates in Cairo on July 3, 2013 after a broadcast confirming that the army will temporarily be taking over from the country's first democratically elected president Mohammed Morsi. AFP PHOTO / KHALED DESOUKI

A police general said that security forces have issued arrest warrants for 300 leaders and members of his Muslim Brotherhood movement.

Police have already arrested Saad al-Katatni, head of Mr Morsi's Freedom and Justice Party, and Rashad Bayoumi, the Muslim Brotherhood's deputy supreme guide, the general said.

Hours after the military announced it had cancelled the constitution and would appoint the head of Egypt's top court as interim president, Mr Morsi issued a defiant call to arms in a prerecorded speech aired on Al-Jazeera television.

An Egyptian family celebrates in Cairo on July 3, 2013 after a broadcast confirming that the army will temporarily be taking over from the country's first democratically elected president Mohammed Morsi. AFP PHOTO / KHALED DESOUKI

Four Morsi supporters have been killed in clashes with the army and police in the western city of Marsa Matruh.

Another 10 people were injured after the group of armed supporters stormed the city's security headquarters, the official said.

Egyptians hug and kiss an army soldier after a broadcast confirming the army will temporarily be taking over from the country's first democratically elected president Mohammed Morsi. Picture: AFP PHOTO/MOHAMED EL-SHAHED

Another Morsi supporter was killed in clashes in the coastal city of Alexandria.

Clashes between security forces and Mr Morsi supporters also erupted in the central province of Asiut and the Nile Delta province of Gharbiya.

Egyptians carry police officers on their shoulders as they celebrate the end of Morsi's rule. Picture: AFP PHOTO/MOHAMED EL-SHAHED

Jubilant crowds of tens of thousands, cheered, ignited firecrackers and honked horns soon after the army announced President Mohamed Morsi's rule was over, ending Egypt's worst crisis since its 2011 revolt.

Consultations start "now" for a new Egyptian government after the military deposed president Mohamed Morsi, opposition leader Amr Mussa said.

"Consultations will start from now, for a government and reconciliation," said the former Arab League chief, who ran unsuccessfully against Mr Morsi for the presidency last year.

The Department of Foreign Affairs of Trade (DFAT) says 730 Australians are registered as currently being in the country but estimates the real number is likely to be much higher. A further 822 Australians have registered plans to travel there in the coming weeks.

The Australian embassy in Cairo remains open.

Egyptian children hold national flags as they pose for pictures near army soldiers on an armoured personnel carrier (APC) in a Cairo street.

MILITARY RULERS REASSURE OBAMA

US President Barack Obama said he was "deeply concerned'' over the Egyptian military's ouster of president Mohamed Morsi and urged a quick return to elected civilian government.

He also said he had ordered a review of the legal implications for US aid to Egypt in the wake of the military's toppling of the country's first democratically elected leader.

Egyptian military leaders have sought to assure the Obama administration that they are not interested in long-term rule following their toppling of President Mohammed Morsi and have appointed a government of civilian technocrats to temporarily run the country in an apparent bid to forestall potential US sanctions, American officials said.

CNN correspondent Ivan Watson tweets a picture of Egyptian soldiers praying on the Jemaa bridge across the nile River at sunset in Cairo.

US law requires the administration to suspend its $1.5 billion in annual military and economic assistance to Egypt - which is deemed a critical U.S. national security priority - if the ouster is determined to have been a coup d'etat.

Under the law, the unconstitutional ouster of a democratically elected government by a country's armed forces would trigger an aid cutoff. But the administration can take time to make that legal determination, and officials said they believed Egypt's military was trying to take steps to keep such a finding from being reached.

The US government has not called Mr Morsi's ouster a coup.

The senator who leads the Senate Appropriations panel that oversees foreign aid, Senator Patrick Leahy, said in a statement that the committee will review future assistance to Egypt as it awaits what he calls "a clearer picture'' of the situation. Senator Leahy also said Mr Morsi squandered an historic opportunity.

Opponents of Egypt's Islamist President Mohammed Morsi shout slogans during a protest in Tahrir Square in Cairo, Egypt.

UN leader Ban Ki-moon understands Egyptians have "deep frustrations" but expressed concern over the military's ouster of president Mohamed Morsi, a spokesman said.

Mr Ban believes that "military interference in the affairs of any state is of concern," said deputy UN spokesman Eduardo del Buey.

French Foreign Minister Laurent Fabius said Paris has taken note that elections had been announced in Egypt following a transition period after the army ousted president Mohamed Morsi.

"In a situation that has worsened seriously and with extreme tension in Egypt, new elections have finally been announced, after a transition period," Mr Fabius said in a statement. "France takes note of it."

France hoped a timetable would be drawn up respecting "civil peace, pluralism, individual liberties and the achievements of the democratic transition, so that the Egyptian people can freely choose their leaders and their future", he added.

Saudi King Abdullah sent a message of congratulations to Egypt's new caretaker president, saying his appointment comes at a "critical" time in the nation's history, the official Saudi news agency SPA reported.

"On behalf of the people of Saudi Arabia I congratulate you for taking over the leadership of Egypt at this critical time in its history," King Abdullah said in the first message of congratulations by an Arab leader to Adli Mansour.

EU foreign policy chief Catherine Ashton has called for a swift return to democracy in Egypt after the army deposed Mr Morsi.

"I am following closely developments in Egypt and am fully aware of the deep divisions in society, popular demands for political change and efforts at brokering a compromise," she said in a statement.

"I urge all sides to rapidly return to the democratic process, including the holding of free and fair presidential and parliamentary elections and the approval of a constitution."

In London, Britain urged for calm and spoke out against the use of military intervention in bringing about regime change, but stopped short of calling it a coup.

"The situation is clearly dangerous and we call on all sides to show restraint and avoid violence," Foreign Secretary William Hague said in a statement.

Despite its concerns about the dramatic events, Britain called on all parties to move forward and "show the leadership and vision needed to restore and renew Egypt's democratic transition.

SITUATION REMAINS VOLATILE

Camped out in Cairo's iconic Tahrir Square for a week, the anti-Morsi protesters let loose with an outburst of joy when military chief General Adel Fattah al-Sisi brought them the news they all were waiting to hear.

As the din rang out for over an hour in Tahrir, epicentre of the Arab Spring uprising that ousted dictator Hosni Mubarak, groups of overjoyed revellers carried members of the security forces on their shoulders as heroes.

Across town near Nasr City, where Morsi's Islamists had gathered in a counter-demonstration, one celebrator Omar Sherif said: "It's a new historical moment. We get rid of Morsi and the Muslim Brotherhood".

He takes the helm of a nation riven by deep divisions over the army's ouster of its first freely elected president Mohamed Morsi following days of deadly clashes between his Islamist supporters and their increasingly numerous opponents.

Ironically he was named by Mr Morsi himself to Egypt's top judicial post, which, following the army's suspension of the constitution, catapulted him into political power.

US EMBASSY PULLS OUT

Meanwhile the US embassy in Cairo has been on "ordered departure" status for non-emergency staff and dependents all employees. That means that those covered by the order are required to leave the country.

It was not immediately clear if an evacuation operation would be mounted or if those departing would use commercial airlines or passenger ships to leave.

The BBC has reported the Muslim Brotherhood TV station has been taken off the air and its staff arrested, there are also reports that Al-Jazeera's Egypt service has also been shut down during a live broadcast and troops have stormed the building.

MORSI INSISTS HE IS STILL PRESIDENT

But Mr Morsi's office has rejected the move as "illegal'' and called on Egyptians to peacefully resist the "coup'' and the overthrown leader himself insisted in an amateur video posted on the internet that he remains Egypt's president.

"I am the elected president of Egypt," the Islamist politician said in the video uploaded to YouTube.

"It is now demanded of the people to defend this legitimacy and... for legitimacy to be constitutional," he added in reference to his election a year ago and a constitutional referendum in December.

But the coup potentially throws the country into further confrontation.

Mr Morsi, Egypt's first freely elected president, came under massive pressure in the run-up to Sunday's anniversary of his maiden year in office, with his opponents accusing him of failing the 2011 revolution by concentrating power in Islamist hands.

The embattled 62-year-old proposed a "consensus government'' as a way out of the country's worst crisis since the 2011 uprising ended three decades of authoritarian rule by Hosni Mubarak.

But the United States urged Mr Morsi to "do more'' as a military deadline passed for him to meet the demands of the people following a week of bloody unrest during mass protests calling for him to quit.

DOWNFALL ANNOUNCEMENT

Opposition leader Mohamed ElBaradei, the UN nuclear watchdog chief, and the heads of the Coptic Church and Al-Azhar, Sunni Islam's highest seat of learning, sat alongside the armed forces chief as he announced Mr Morsi's ouster on state television.

Pres. Morsy urges civilians and military members to uphold the law & the Constitution not to accept that coup which turns #Egypt backwards

The choreography was designed to show broad civilian support for the military's move to topple Mr Morsi, Egypt's first freely elected leader, dashing the hopes of supporters who had seen his elevation to the presidency after years underground as one of the key achievements of the 2011 revolution.

The road map revealed plans for an interim administration, of up to one year, which would include the head of the supreme constitutional court and a senior army figure.

The constitution, controversially approved by Mr Morsi's Islamist allies in December, would be suspended for up to 12 months while a new one was drawn up and put to a referendum, before presidential and parliamentary elections.

In a statement before he was overthrown, Mr Morsi warned that his electoral legitimacy is the only safeguard against violence and instability.

"The presidency envisions the formation of a consensus coalition government to oversee the next parliamentary election,'' Mr Morsi's office said on Facebook.

He refused to meet the 5pm (1am AEST) deadline from the military for him to step down.

By 6:30pm (2:30am AEST) military forces began surrounding Cairo. Tanks and troops headed for the presidential palace - although it was unclear whether Mr Morsi was inside

The US State Department had expressed concern about what was happening in Egypt but has not spoken since news he was overthrown.

Thousands of people gathered in Nasr City in a show of support for Mr Morsi, despite an attack that killed 16 of them and injured 200 overnight.

That spate of bloodletting took to almost 50 the number of people killed in Egypt since the latest crisis flared a week ago ahead of Sunday's anniversary of Mr Morsi's swearing-in.

In his emotional, 46-minute address aired live to the nation late on Tuesday, Mr Morsi accused loyalists of his ousted autocratic predecessor Hosni Mubarak of exploiting the wave of protests to topple his regime and thwart democracy.

"There is no substitute for legitimacy,'' said Mr Morsi, at times angrily raising his voice, thrusting his fist in the air and pounding the podium. He warned that electoral and constitutional legitimacy "is the only guarantee against violence.''

With broad grins, they sang patriotic songs they have become accustomed to hearing as the same tunes have been pumped out on state television in the weeks leading up to the crisis.

"Morsi deserves his end. He was the president of the Muslim Brotherhood, not of Egypt,'' said Cairo resident Amr Mohammed, who carried his 40-day-old daughter in his arms as he marched to the Ittihadiya presidential palace.

A group of housewives put a table in the street and handed out dates and free cups of water, as celebrations erupted when it appeared that Mr Morsi would not survive the military coup.

Upon hearing the rumour, one elderly man kneeled down on an Egyptian flag and said "Allahu Akbar'' (God is greatest).

Nehal Serry, a woman who helped to organise the refreshments, said: "This is for the sake of Egypt. We are celebrating that we are getting rid of Morsi''.

On Monday, the military gave Mr Morsi an ultimatum to meet the protesters' demands within 48 hours. If not, the generals' plan would suspend the Islamist-backed constitution, dissolve the Islamist-dominated legislature and set up an interim administration headed by the country's chief justice, which is what they have done.

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